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It was a fairly common practice in Pepys' day to use characters that were not part of the standard alphabet in one's ciphers. In addition to a simple substitution scheme (where, for instance, a=l, b=m, c=n, etc.), other original, i.e., non-alphabetical, symbols might be used to replace common words such as 'and', 'the', 'with' etc. There would probably also be nulls (symbols that stood for nothing at all, designed to confuse the enemy cryptologist) and possibly also a dowbleth (a symbol indicating that the next character should be read as a double letter).

I hope for Pepys' sake that his cipher was a good one, although I doubt it was as cleverly nasty as the Great Cipher used by Louis XIV’s spymasters, Antoine and Bonaventure Rossignol (father and son), which after their deaths (they had not passed its secrets on to anyone else) was not broken until the 1890s. (For more fascinating information about the history cryptography, I recommend "The Code Book: the Evolution of Secrecy from Mary Queen of Scots to Quantum Cryptography", by Simon Singh.)

sipher, cyfer, cifer, ciphre, sypher, ziphre, scypher, cyphar, cyphre, ciphar, zifer, cypher. Francis Bacon who wrote about it spelled it as ciphras in Latininteresting 16/17 century (j bonds galore) spies etc.,"...science of cryptology was not taken seriously at least on the royalist side until very late..."http://home.att.net/~tleary/cryptolo.htm"... lines are from Bishop John Wilkins MERCURY the Secret and Swift Messenger 1641 .." should be read

Ciphers from Grahamt 9 may one gets another in put about cyphers http://www-gap.dcs.st-and.ac.uk/~history/Mathem...Wallis in 1642 -.".. one evening at supper, a letter in cipher was brought in, relating to the capture of Chichester on 27 December 1642, which Wallis in two hours succeeded in deciphering. The feat made his fortune..."